WO2023023635A1 - Génération non virale de lymphocytes t porteurs de récepteurs antigéniques chimériques obtenus par édition génique - Google Patents

Génération non virale de lymphocytes t porteurs de récepteurs antigéniques chimériques obtenus par édition génique Download PDF

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WO2023023635A1
WO2023023635A1 PCT/US2022/075193 US2022075193W WO2023023635A1 WO 2023023635 A1 WO2023023635 A1 WO 2023023635A1 US 2022075193 W US2022075193 W US 2022075193W WO 2023023635 A1 WO2023023635 A1 WO 2023023635A1
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cells
car
cell
transgene
gene
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Krishanu Saha
Christian Matthew Capitini
Katherine Paige Mueller
Nicole Jenine Piscopo
Amritava DAS
Matthew Hull Forsberg
Louise Armie Saraspe
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Wisconsin Alumni Research Foundation
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Priority to CA3229450A priority Critical patent/CA3229450A1/fr
Publication of WO2023023635A1 publication Critical patent/WO2023023635A1/fr

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    • C07—ORGANIC CHEMISTRY
    • C07K—PEPTIDES
    • C07K14/00—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof
    • C07K14/435—Peptides having more than 20 amino acids; Gastrins; Somatostatins; Melanotropins; Derivatives thereof from animals; from humans
    • C07K14/705—Receptors; Cell surface antigens; Cell surface determinants
    • C07K14/70503—Immunoglobulin superfamily
    • C07K14/7051—T-cell receptor (TcR)-CD3 complex
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/461—Cellular immunotherapy characterised by the cell type used
    • A61K39/4611—T-cells, e.g. tumor infiltrating lymphocytes [TIL], lymphokine-activated killer cells [LAK] or regulatory T cells [Treg]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/463—Cellular immunotherapy characterised by recombinant expression
    • A61K39/4631—Chimeric Antigen Receptors [CAR]
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K39/00—Medicinal preparations containing antigens or antibodies
    • A61K39/46—Cellular immunotherapy
    • A61K39/464—Cellular immunotherapy characterised by the antigen targeted or presented
    • A61K39/4643—Vertebrate antigens
    • A61K39/4644—Cancer antigens
    • A61K39/464469—Tumor associated carbohydrates
    • A61K39/464471—Gangliosides, e.g. GM2, GD2 or GD3
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
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    • C12N15/00—Mutation or genetic engineering; DNA or RNA concerning genetic engineering, vectors, e.g. plasmids, or their isolation, preparation or purification; Use of hosts therefor
    • C12N15/09—Recombinant DNA-technology
    • C12N15/11—DNA or RNA fragments; Modified forms thereof; Non-coding nucleic acids having a biological activity
    • C12N15/113—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing
    • C12N15/1138—Non-coding nucleic acids modulating the expression of genes, e.g. antisense oligonucleotides; Antisense DNA or RNA; Triplex- forming oligonucleotides; Catalytic nucleic acids, e.g. ribozymes; Nucleic acids used in co-suppression or gene silencing against receptors or cell surface proteins
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N5/00—Undifferentiated human, animal or plant cells, e.g. cell lines; Tissues; Cultivation or maintenance thereof; Culture media therefor
    • C12N5/06—Animal cells or tissues; Human cells or tissues
    • C12N5/0602—Vertebrate cells
    • C12N5/0634—Cells from the blood or the immune system
    • C12N5/0636—T lymphocytes
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N9/00—Enzymes; Proenzymes; Compositions thereof; Processes for preparing, activating, inhibiting, separating or purifying enzymes
    • C12N9/14—Hydrolases (3)
    • C12N9/16—Hydrolases (3) acting on ester bonds (3.1)
    • C12N9/22—Ribonucleases RNAses, DNAses
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2239/00—Indexing codes associated with cellular immunotherapy of group A61K39/46
    • A61K2239/31—Indexing codes associated with cellular immunotherapy of group A61K39/46 characterized by the route of administration
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2239/00—Indexing codes associated with cellular immunotherapy of group A61K39/46
    • A61K2239/38—Indexing codes associated with cellular immunotherapy of group A61K39/46 characterised by the dose, timing or administration schedule
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K2239/00—Indexing codes associated with cellular immunotherapy of group A61K39/46
    • A61K2239/46—Indexing codes associated with cellular immunotherapy of group A61K39/46 characterised by the cancer treated
    • A61K2239/47—Brain; Nervous system
    • A—HUMAN NECESSITIES
    • A61—MEDICAL OR VETERINARY SCIENCE; HYGIENE
    • A61K—PREPARATIONS FOR MEDICAL, DENTAL OR TOILETRY PURPOSES
    • A61K48/00—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy
    • A61K48/005—Medicinal preparations containing genetic material which is inserted into cells of the living body to treat genetic diseases; Gene therapy characterised by an aspect of the 'active' part of the composition delivered, i.e. the nucleic acid delivered
    • C—CHEMISTRY; METALLURGY
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    • C12N2310/00—Structure or type of the nucleic acid
    • C12N2310/10—Type of nucleic acid
    • C12N2310/20—Type of nucleic acid involving clustered regularly interspaced short palindromic repeats [CRISPRs]
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
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    • C12N2510/00—Genetically modified cells

Definitions

  • the present disclosure is related to method of preparing genome-edited T cells, particular chimeric antigen receptor (CAR) T cells.
  • CAR chimeric antigen receptor
  • CAR T cells chimeric antigen receptor
  • CAR T cells chimeric antigen receptor
  • the use of viral vectors for CAR T cell manufacturing constitutes a bottleneck in the supply chain for biomanufacturing and can be problematic due to (7) batch-to-batch variability, (2) use of xenogeneic components during manufacturing of viral vectors, and (3) the high random integration of viral elements into the human genome.
  • the poorly specified integration of the CAR transgene can lead to heterogeneous expression that can be readily silenced, in part by host cell recognition of viral genetic elements.
  • Methods to generate CAR T cells generally involve viral vectors, transposons or transient transfection.
  • Autologous CAR T cells are traditionally generated using lenti viruses or retroviruses. They can also be generated using transposon-based systems. All of these systems randomly integrate the CAR transgene throughout the human genome. More recently, transfection with mRNA encoding the CAR has also been reported, however the limited half-life of mRNA ultimately does not provide a durable CAR therapy past a few days to weeks.
  • Genome editing has been used to generate CAR T cells with a site-specific integration of the CAR, however these methods rely on transduction of the T cells with AAVs.
  • AAV6 has been used to deliver the homology directed repair template that encodes the CAR. This was recently demonstrated for a CD 19 CAR appropriate for treatment of hematologic malignancies, but not solid tumors.
  • methods to generate CAR T cells have shown limited to no activity in solid tumors. What is needed are new methods for generating genetically modified T cells, such as CAR T cells, that would lead to measurable efficacy against either hematologic malignancies or solid tumors.
  • an ex vivo, non- viral method of site-specifically inserting a transgene containing a chimeric antigen receptor (CAR) gene into a T cell expressed gene to generate CAR T cells comprising preparing a non- viral double- stranded homology-directed repair (HDR) template comprising the transgene flanked by homology arms that are complementary to sequences on both sides of a cleavage site in the T cell expressed gene, introducing into a population of unmodified T cells a Cas9 ribonucleoprotein (RNP) and the double-stranded HDR template, to provide the CAR T cells wherein the Cas9 RNP comprises a Cas9 protein and a guide RNA that directs double stranded DNA cleavage of a cleavage site in the T cell expressed gene, wherein the non- viral double-stranded HDR template contains the transgene sequence flanked by homology arms that are complementary to sequences on both sides of the HDR
  • a non- viral produced CAR T cell has a genome having a CAR sequence specifically integrated into a T cell expressed gene, wherein the T cell is enriched for the CD62L and/or CD45RA markers indicative of naive and stem cell memory phenotypes compared to viral-produced control CAR T cells.
  • a non- viral produced CAR T cell has a genome having a CAR sequence specifically integrated into a T cell expressed gene, wherein the T cell has reduced expression of TIM3 and/or LAG3 markers of T cell exhaustion compared to viral- produced control CAR T cells.
  • a method of treating a subject comprises administering any of the foregoing CAR T cells to a subject in need of adoptive T cell therapy.
  • FIG. la is a schematic showing the CAR genetic construct and nonviral strategy to insert the CAR into the first exon of the human TRAC locus.
  • the seed sequence of the gRNA is identified and the protospacer adjacent motif (PAM) for SpyCas9 is underlined (SEQ ID NOS. 2 and 3).
  • PAM protospacer adjacent motif
  • LHA left homology arm
  • SA splice acceptor
  • 2A self-cleaving peptide
  • pA rabbit B-globin polyA terminator.
  • FIG. lb is a summary of manufacturing schedule and analyses for all cell products.
  • FIG. 1c shows representative density flow cytometry plots for transgene and TCR surface protein levels on the manufactured cell products.
  • Y-axis shows CAR or mCherry transgene levels and
  • X-axis shows TCR levels on day 7 post isolation (day 5 postelectroporation for NV-CAR and NV-mCh, and day 4 post viral transfection for control RV- CAR). Boxes show populations selected for downstream analysis in FIG. Id-f.
  • FIG. 1c shows representative density flow cytometry plots for transgene and TCR surface protein levels on the manufactured cell products.
  • Y-axis shows CAR or mCherry transgene levels
  • X-axis shows TCR levels on day 7 post isolation (day 5 postelectroporation for NV-CAR and NV-mCh, and day 4 post viral transfection for control RV- CAR). Boxes show populations selected for downstream analysis in FIG. Id-f.
  • Id shows histograms show CAR expression for the three test groups. Boxplots show the percentage of CAR positive cells in each sample, and mean fluorescence intensity (MFI) values for the CAR expression levels, respectively.
  • FIG. If shows histograms show CD62L expression for the three test groups. Boxplots show mean fluorescence intensity (MFI) for CD62L expression.
  • FIG. Ih shows a Manhattan plot of CHANGE-seq- detected on- and off-target sites organized by chromosomal position with bar heights representing CHANGE-seq read count. The on-target site is indicated with the arrow.
  • FIG. Ih shows a Manhattan plot of CHANGE-seq
  • FIG. Ij shows UMAP projections as in j showing only cells for which transgene -positive cells were detected. Transgene-positive cells cluster similarly for both NV-CAR and RV-CAR T cells, but not NV-mCh T cells.
  • lk.l, k.2 and k.3, show enrichment of Reactome pathway gene signatures (rows) in the transgenepositive cells from donors 1 and 2.
  • NES Normalized Enrichment Score.
  • GSEA representative gene set enrichment analysis
  • FIG. 2a-i show nonviral CRISPR-CAR T cells exhibit a robust cytotoxic response to target antigen-positive tumor cells in vitro and induce tumor regression in vivo with a reduced exhaustion phenotype.
  • FIG. 2b shows IncuCyte in vitro assay of T cell potency, averaged across donors.
  • AnnexinV was added as a marker of cell death; y-axis shows GFP- positive cancer cells in each well of a 96- well plate. The ratio of T cells to cancer cells is 5:1. The consistent decrease in CHLA20 cells after 15 hours indicates high potency of both NV- CAR and RV-CAR T cells.
  • FIG. 2c shows a UMAP projections as in c showing only cells for which transgene was detected. Transgene-positive cells cluster similarly for both NV-CAR and RV-CAR T cells, but not for NV-mCh T cells.
  • 2d.l, d.2, and d.3 show enrichment of Reactome pathway gene signatures (rows) in the transgene-positive cells from donors 1 and 2 after co-culture with GD2-positive CHLA20 cancer cells.
  • NES Normalized Enrichment Score.
  • representative GSEA showing differential cytotoxicity signature of NV- CAR/NV-mCh paired samples for two donors, and NV-CAR/RV-CAR samples.
  • NV-CAR T cells show significant upregulation of cytotoxicity markers relative to NV-mCh control cells after GD2 antigen exposure, while NV-CAR and RV-CAR T cells show no significant difference in activation signature upon GD2 antigen stimulation.
  • FIG. 2e shows a schematic of the in vivo mouse dosing strategy using NSG mice harboring GD2-positive CHLA20 neuroblastoma tumors.
  • FIG. 2f shows representative IVIS images of NSG mice with CHLA20 tumors that were treated with either 10 million NV-CAR, RV-CAR, or NV-mCh T cells.
  • FIG. 2i shows box plots on the amount of human T cells present in mouse spleens, as measured by the presence of human CD45 using flow cytometry, and the percentage of those cells in the spleen that were CAR-positive.
  • Figure 3a-e shows pre-antigen exposure characterization of NV-CAR T cells.
  • Fig 3 a shows left, viability of cells throughout the manufacturing timeline, pooled for all 4 donors.
  • Fig 3c shows the level of TCR disruption in NV-CAR and NV-mCh T cells measured by both TCR surface expression by flow cytometry (right) and presence of indels at the TRAC locus (left).
  • Fig. 3d shows percent of cells with indels at the TRAC locus in both NV-CAR and NV-mCh conditions.
  • Figure 4a-c show single cell transcriptomic characterization across eleven samples shows distinct transcriptional signatures associated with CAR expression but not mCherry expression, both before and after antigen exposure.
  • Figure 4 b shows a UMAP projection as in Fig 4a, separated to show clustering of transgene positive cells prior to antigen exposure (left) and after 24 hours of in vitro exposure to GD2+ CHLA20 neuroblastoma.
  • Fig. 4c shows a UMAP projection as in Fig. 4a, showing transgene positive cells for each individual sample.
  • CAR-positive cells from NV-CAR and RV-CAR groups consistently cluster regardless of the presence of GD2 antigen, while NV-mCh cells do not, suggesting a distinct transcriptional profile associated with CAR signaling.
  • Figure 5 shows a novel plasmid used to generate CAR HDR template via PCR.
  • the PCR primers were designed to amplify the following: TRAC LHA-SA-2A-14g2a- hinge-CD28-OX40-zeta chain-rb_glob_PA_terminator-TRAC RHA.
  • LHA left homology arm
  • SA splice acceptor: 2A: self-cleaving peptide
  • rb_glob_PA_terminator rabbit beta globin polyA terminator.
  • Figure 6 shows representative images of NV-CRISPR CAR T cells postediting.
  • Figure 7 shows a flow cytometry plot with representative gene editing. TCR expression is shown on the X axis, and CAR expression is on the Y axis, with 94% TCR knockout and 46% CAR knockin.
  • Figure 8 shows average gene editing efficiency across 20 replicates per cell type. 20 replicate NV-CAR and NV-mCherry editing experiments yielded an average knockin efficiency of 35% in both conditions, as measured by flow cytometry. Unedited controls show no non-specific staining.
  • Described herein are methods to generate genome edited T cells such as CAR T cells using site-specific genome editing where the editing machinery consists only of proteins and nucleic acids without any viral vectors.
  • CRISPR-Cas9 mediated genomic insertion of CAR transgenes into the T cell receptor alpha constant, TRAC, locus in primary human T cells collected from healthy donors.
  • These cells termed nonviral- (NV)-TRAC-CAR T cells, exhibit proper TRAC -specific integration of the CAR transgene, robust gene expression of the CAR mRNA, and translated CAR proteins on the T cell surface.
  • NV 77MC-CAR T cells potently upregulate cytotoxic transcriptional programs and kill target-antigen-positive human cancer cells in vitro within co-culture assays
  • the NV 7 AC-CAR T cells successfully cause tumor regression in vivo within human xenograft cancer models in mice at comparable efficiency to state-of-the-art, viral CAR T cells.
  • NV- 77MC-CAR T cells can be manufactured in a xeno-free manner and have high potential to simplify and advance CAR T cell manufacturing by elimination of viral vectors.
  • an ex vivo method of site-specifically inserting a synthetic DNA sequence, e.g., a transgene containing a chimeric antigen receptor (CAR) gene, into a T cell genome comprises introducing into a population of unmodified T cells a Cas9 ribonucleoprotein (RNP) and a non-viral double-stranded homology-directed repair (HDR) template, to provide genome-edited T cells.
  • the Cas9 RNP comprises a Cas9 protein and a guide RNA that directs double stranded DNA cleavage of a cleavage site in a T-cell expressed gene.
  • the non-viral double-stranded HDR template comprises a synthetic DNA sequence flanked by homology arms that are complementary to sequences on both sides of the cleavage site in the T cell expressed gene.
  • the synthetic DNA sequence is specifically integrated into the cleavage site of the T cell expressed gene by the Cas9 ribonucleoprotein in the genome-edited T cells.
  • the method includes culturing the genome- edited T cells in xeno-free medium to provide a cultured population of genome-edited T cells having the synthetic DNA sequence specifically integrated in the T-cell expressed gene locus.
  • an endogenous promoter of the T cell expressed gene drives expression of the synthetic DNA sequence
  • the synthetic DNA sequence includes a promoter that drives expression of the synthetic DNA sequence.
  • a synthetic DNA sequence is site- specific ally inserted into the genome of a T cell, specifically into a T cell expressed gene.
  • a synthetic DNA sequence is a DNA sequence that is not native to the genome of the T cell to be modified.
  • An exemplary aspect of a synthetic DNA sequence is a “chimeric antigen receptor (CAR)”.
  • CAR refers to a recombinant fusion protein that has an antigenspecific extracellular domain coupled to an intracellular domain that directs the cell to perform a specialized function upon binding of an antigen to the extracellular domain.
  • a CAR comprises an antigen-specific extracellular domain (e.g., a single chain variable fragment [scFV] that can bind a surface-expressed antigen of a malignancy) coupled to an intracellular domain (e.g., CD28, ICOS, CD27, 4-1BB, 0X40, CD40L, or CD3-Q by a transmembrane domain (e.g., derived from a CD4, CD8a, CD28, IgG or CD3- ⁇ transmembrane domain).
  • an antigen-specific extracellular domain e.g., a single chain variable fragment [scFV] that can bind a surface-expressed antigen of a malignancy
  • an intracellular domain e.g., CD28, ICOS, CD27, 4-1BB, 0X40, CD40L, or CD3-Q
  • a transmembrane domain e.g., derived from a CD4, CD8a, CD28, IgG or
  • the length of the homology arms influences the efficiency of synthetic DNA sequence integration.
  • the homology arms are 400 to 1000 base pairs, specifically 450 to 750 base pairs long.
  • the antigen- specific extracellular domain of a CAR recognizes and specifically binds an antigen, typically a surface-expressed antigen of a malignancy.
  • An antigen- specific extracellular domain specifically binds an antigen when, for example, it binds the antigen with an affinity constant or affinity of interaction (KD) between about 0.1 pM to about 10 pM, specifically about 0.1 pM to about 1 pM, more specifically about 0.1 pM to about 100 nM.
  • KD affinity constant or affinity of interaction
  • An antigen-specific extracellular domain suitable for use in a CAR may be any antigenbinding polypeptide, one or more scFv, or another antibody based recognition domain (cAb VHH (camelid antibody variable domains) or humanized versions thereof, IgNAR VH (shark antibody variable domains) and humanized versions thereof, sdAb VH (single domain antibody variable domains) and “camelized” antibody variable domains are suitable for use.
  • T cell receptor (TCR) based recognition domains such as single chain TCR may be used as well as ligands for cytokine receptors.
  • the present disclosure provides chimeric antigen receptors (CARs) that bind to an antigen of interest.
  • the CAR can bind to a tumor antigen or a pathogen antigen.
  • the CAR binds to a tumor antigen.
  • Any tumor antigen (antigenic peptide) can be used in the tumor-related embodiments described herein.
  • Sources of antigen include, but are not limited to, cancer proteins.
  • the antigen can be expressed as a peptide or as an intact protein or portion thereof.
  • the intact protein or a portion thereof can be native or mutagenized.
  • tumor antigens include carbonic anhydrase IX (CAIX), carcinoembryonic antigen (CEA), CD8, CD7, CD10, CD19, CD20, CD22, CD30, CD33, CLL1, CD34, CD38, CD41, CD44, CD49f, CD56, CD74, CD133, CD138, CD123, CD44V6, an antigen of a cytomegalovirus (CMV) infected cell (e.g., a cell surface antigen), epithelial glycoprotein-2 (EGP-2), epithelial glycoprotein- 40 (EGP-40), epithelial cell adhesion molecule (EpCAM), receptor tyrosine-protein kinases erb-B2,3,4 (erb-B2,3,4), folate-binding protein (FBP), fetal acetylcholine receptor (AChR), folate receptor-a, Ganglioside G2 (GD2), Ganglioside G3 (GD3), human Epidermal
  • CMV
  • the CAR binds to a pathogen antigen, e.g., for use in treating and/or preventing a pathogen infection or other infectious disease, for example, in an immunocompromised subject.
  • pathogen include viruses, bacteria, fungi, parasite and protozoa capable of causing disease.
  • Retroviridae e.g. human immunodeficiency viruses, such as HIV-1 (also referred to as HDTV-III, LAVE or HTLV- III/LAV, or HIV-III; and other isolates, such as HIV-LP; Picornaviridae (e.g. polio viruses, hepatitis A virus; enteroviruses, human Coxsackie viruses, rhinoviruses, echoviruses); Calciviridae (e.g. strains that cause gastroenteritis); Togaviridae (e.g. equine encephalitis viruses, rubella viruses); Flaviridae (e.g.
  • Coronoviridae e.g. coronaviruses
  • Rhabdoviridae e.g. vesicular stomatitis viruses, rabies viruses
  • Filoviridae e.g. ebola viruses
  • Paramyxoviridae e.g. parainfluenza viruses, mumps virus, measles virus, respiratory syncytial virus
  • Orthomyxoviridae e.g. influenza viruses
  • Bungaviridae e.g. Hantaan viruses, bunga viruses, phlebo viruses and Naira viruses
  • Arena viridae hemorrhagic fever viruses
  • Reoviridae e.g.
  • reoviruses reoviruses, orbiviurses and rotaviruses
  • Birnaviridae Hepadnaviridae (Hepatitis B virus); Parvovirida (parvoviruses); Papovaviridae (papilloma viruses, polyoma viruses); Adenoviridae (most adenoviruses); Herpesviridae (herpes simplex virus (HSV) 1 and 2, varicella zoster virus, cytomegalovirus (CMV), herpes virus; Poxviridae (variola viruses, vaccinia viruses, pox viruses); and Iridoviridae (e.g. African swine fever virus); and unclassified viruses (e.g.
  • Non-limiting examples of bacteria include Pasteurella, Staphylococci, Streptococcus, Escherichia coli, Pseudomonas species, and Salmonella species.
  • infectious bacteria include but are not limited to, Helicobacter pyloris, Borelia burgdorferi, Legionella pneumophilia, Mycobacteria sps (e.g., M. tuberculosis, M. avium, M. intracellulare, M. kansaii, M.
  • the pathogen antigen is a viral antigen present in Cytomegalovirus (CMV), a viral antigen present in Epstein Barr Virus (EBV), a viral antigen present in Human Immunodeficiency Virus (HIV), or a viral antigen present in influenza virus.
  • CMV Cytomegalovirus
  • EBV Epstein Barr Virus
  • HAV Human Immunodeficiency Virus
  • influenza virus a viral antigen present in influenza virus.
  • the intracellular domain transmits the T cell activation signal.
  • the intracellular domain can increase CAR T cell cytokine production and facilitate T cell replication.
  • the intracellular domain reduces CAR T cell exhaustion, increases T cell antitumor activity, and enhances survival of CAR T cells in patients.
  • Exemplary intracellular domains, also call co-stimulatory domains, include CD28, ICOS, CD27, 4-1BB, 0X40, CD40L, and CD3-
  • the antigen-specific extracellular domain is linked to the intracellular domain of the CAR by a transmembrane domain, e.g., derived from a CD4, CD8a, CD28, IgG or CD3- ⁇ transmembrane domain.
  • the transmembrane domain traverses the cell membrane, anchors the CAR to the T cell surface, and connects the extracellular domain to the intracellular signaling domain, thus impacting expression of the CAR on the T cell surface.
  • CARs may also further comprise one or more costimulatory domain and/or one or more spacer.
  • a costimulatory domain is derived from the intracellular signaling domains of costimulatory proteins that enhance cytokine production, proliferation, cytotoxicity, and/or persistence in vivo.
  • a spacer or hinge connects (i) the antigen-specific extracellular domain to the transmembrane domain, (ii) the transmembrane domain to a costimulatory domain, (Hi) a costimulatory domain to the intracellular domain, and/or (iv) the transmembrane domain to the intracellular domain.
  • inclusion of a spacer domain e.g.
  • IgGl, IgG2, IgG4, CD28, CD8 may affect flexibility of the antigen-binding domain and thereby CAR function.
  • Suitable transmembrane domains, costimulatory domains, and spacers are known in the art.
  • synthetic DNA sequences within the HDRT could incorporate synthetic receptors, cytokine signaling, and short hairpin (sh)RNA.
  • synthetic receptors e.g., modified interleukin (IL)- 13 sequences
  • natural ligand-binding domains of receptors e.g., NKG2D and CD27
  • sequences that encode cytokine receptor signaling important for T cell maintenance and expansion e.g., IL-2 receptor beta chain (IL-2Rb) and a STAT3-binding motif.
  • sh(RNA) could also be expressed from the synthetic DNA sequence that helps provide control over the edited T cell behavior.
  • the synthetic DNA sequence comprises a coding sequence for a fluorescent protein such as mCherry, mKate, GFP, BFP, RFP, CFP, YFP, mCyan, mOrange, tdTomato, mBanana, mPlum, mRaspberry, mStrawberry, and mTangerine.
  • a fluorescent protein such as mCherry, mKate, GFP, BFP, RFP, CFP, YFP, mCyan, mOrange, tdTomato, mBanana, mPlum, mRaspberry, mStrawberry, and mTangerine.
  • a Cas9 RNP and a non-viral double-stranded HDR template including the synthetic DNA sequence are introduced into the unmodified T cells to provide genome-edited T cells.
  • introducing means refers to the translocation of the Cas9 ribonucleoprotein and a non-viral double- stranded HDR template from outside a cell to inside the cell, such as inside the nucleus of the cell. Introducing can include transfection, electroporation, contact with nanowires or nanotubes, receptor mediated internalization, translocation via cell penetrating peptides, liposome mediated translocation, and the like.
  • Unmodified T cells include autologous T cells that are collected from a patient, such as a cancer patient, by peripheral blood draw or leukapheresis. Unmodified T cells can also include T cells from allogeneic healthy donors or induced pluripotent stem cells which can be used to produce universal T cells for administration to a patient. T cells are generally modified ex vivo, that is outside of the patient, and then the modified T cells such as CAR T cells are returned to the patient, such as by intravenous infusion, subcutaneous, intratumoral, intraperitoneal or intracerebral injection.
  • CRISPR refers to the Clustered Regularly Interspaced Short Palindromic Repeats type II system used by bacteria and archaea for adaptive defense. This system enables bacteria and archaea to detect and silence foreign nucleic acids, e.g., from viruses or plasmids, in a sequence- specific manner.
  • guide RNA interacts with Cas9 and directs the nuclease activity of Cas9 to target DNA sequences complementary to those present in the guide RNA.
  • Guide RNA base pairs with complementary sequences in target DNA. Cas9 nuclease activity then generates a double-stranded break in the target DNA.
  • CRISPR/Cas9 is a ribonucleoprotein (RNP) complex.
  • CRISPR RNA includes a 20 base protospacer element that is complementary to a genomic DNA sequence as well as additional elements that are complementary to the transactivating RNA (tracrRNA). The tracrRNA hybridizes to the crRNA and binds to the Cas9 protein, to provide an active RNP complex.
  • the CRISPR/Cas9 complex contains two RNA species.
  • Guide RNA, or gRNA can be in the form of a crRNA/tracrRNA two guide system, or an sgRNA single guide RNA.
  • the guide RNA is capable of directing Cas9- mediated cleavage of target DNA.
  • a guide RNA thus contains the sequences necessary for Cas9 binding and nuclease activity and a target sequence complementary to a target DNA of interest (protospacer sequence).
  • a guide RNA protospacer sequence refers to the nucleotide sequence of a guide RNA that binds to a target genomic DNA sequence and directs Cas9 nuclease activity to a target DNA locus in the genome of the T cell such the TRAC gene, a T cell receptor beta subunit constant gene (TRBC), AAVS1 (i.e., PPP1R12C), TET2, FAS, BID, CTLA4, PDCD1, CBLB, PTPN6, CUT A and B2M genes.
  • the guide RNA protospacer sequence is complementary to the target DNA sequence.
  • “Complementary” or “complementarity” refers to specific base pairing between nucleotides or nucleic acids. Base pairing between a guide RNA and a target region in exon 1 of the TRAC gene can be via a DNA targeting sequence that is perfectly complementary or substantially complementary to the guide RNA. As described herein, the protospacer sequence of a single guide RNA may be customized, allowing the targeting of Cas9 activity to a target DNA of interest.
  • Any desired target DNA sequence of interest may be targeted by a guide RNA target sequence. Any length of target sequence that permits CRISPR-Cas9 specific nuclease activity may be used in a guide RNA. In some embodiments, a guide RNA contains a 20 nucleotide protospacer sequence.
  • the targeted sequence includes a protospacer adjacent motif (PAM) adjacent to the protospacer region which is a sequence recognized by the CRISPR RNP as a cutting site.
  • PAM protospacer adjacent motif
  • the only requirement for a target DNA sequence is the presence of a protospacer-adjacent motif (PAM) adjacent to the sequence complementary to the guide RNA target sequence.
  • PAM protospacer-adjacent motif
  • Different Cas9 complexes are known to have different PAM motifs.
  • Cas9 from Streptococcus pyogenes has a NGG trinucleotide PAM motif; the PAM motif of N. meningitidis Cas9 is NNNNGATT ; the PAM motif of S. thermophilus Cas9 is NNAGAAW ; and the PAM motif of T. denticola Cas9 is NAAAAC.
  • a “Cas9” polypeptide is a polypeptide that functions as a nuclease when complexed to a guide RNA, e.g., an sgRNA or modified sgRNA. That is, Cas9 is an RNA- mediated nuclease.
  • the Cas9 (CRISPR-associated 9, also known as Csnl) family of polypeptides for example, when bound to a crRNA:tracrRNA guide or single guide RNA, are able to cleave target DNA at a sequence complementary to the sgRNA target sequence and adjacent to a PAM motif as described above.
  • Cas9 polypeptides are characteristic of type II CRISPR-Cas systems.
  • Cas9 Cas9 polypeptides include natural sequences as well as engineered Cas9 functioning polypeptides.
  • the term “Cas9 polypeptide” also includes the analogous Clustered Regularly Interspaced Short Palindromic Repeats from Prevotella and Francisella 1 or CRISPR/Cpfl which is a DNA-editing technology analogous to the CRISPR/Cas9 system.
  • Cpfl is an RNA-guided endonuclease of a class II CRISPR/Cas system. This acquired immune mechanism is found in Prevotella and Francisella bacteria.
  • Additional Class I Cas proteins include Cas3, Cas8a, Cas5, Cas8b, Cas8c, Cas lOd, Casel, Cse 2, Csy 1, Csy 2, Csy 3, GSU0054, Cas 10, Csm 2, Cmr 5, CaslO, Csxll, CsxlO, and Csf 1.
  • Additional Class 2 Cas9 polypeptides include Csn 2, Cas4, C2cl, C2c3 and Cas 13a.
  • Exemplary Cas9 polypeptides include Cas9 polypeptide derived from Streptococcus pyogenes, e.g., a polypeptide having the sequence of the Swiss-Prot accession Q99ZW2 (SEQ ID NO: 5); Cas9 polypeptide derived from Streptococcus thermophilus, e.g., a polypeptide having the sequence of the Swiss-Prot accession G3ECR1 (SEQ ID NO: 6); a Cas9 polypeptide derived from a bacterial species within the genus Streptococcus; a Cas9 polypeptide derived from a bacterial species in the genus Neisseria (e.g., GenBank accession number YP_003082577; WP_015815286.1 (SEQ ID NO: 7)); a Cas9 polypeptide derived from a bacterial species within the genus Treponema (e.g., GenBank accession number EMB
  • a putative Cas9 protein may be complexed with crRNA and tracrRNA or sgRNA and incubated with DNA bearing a target DNA sequence and a PAM motif.
  • Cas9 or “Cas9 nuclease” refers to an RNA-guided nuclease comprising a Cas9 protein, or a fragment thereof (e.g., a protein comprising an active, inactive, or partially active DNA cleavage domain of Cas9, and/or the gRNA binding domain of Cas9).
  • a Cas9 nuclease has an inactive (e.g., an inactivated) DNA cleavage domain, that is, the Cas9 is a nickase.
  • both DNA cleavage domains are inactivated. This is referred to as catalytically-inactive Cas9, dead Cas9, or dCas9.
  • editing refers to a change in the sequence of the genome at a targeted genomic location. Editing can include inducing either a double stranded break or a pair of single stranded breaks in the genome, such as in a T cell expressed gene. Editing can also include inserting a synthetic DNA sequence into the genome of the T cell at the site of the break(s).
  • a Cas9 RNP that targets a T cell expressed gene comprises a Cas9 protein and a guide RNA that directs double stranded cleavage of the T cell expressed gene.
  • the guide RNA thus includes a crRNA comprising a single-stranded protospacer sequence and a first complementary strand of a binding region for the Cas9 polypeptide, and a tracrRNA comprising a second complementary strand of the binding region for the Cas9 polypeptide, wherein the crRNA and the tracrRNA hybridize through the first and second complementary strands of the binding region for the Cas9 polypeptide.
  • the single- stranded protospacer region of the guide RNA hybridizes to a sequence in the T cell expressed gene, directing cleavage of the T-cell expressed gene to a specific locus of the T cell expressed gene.
  • Exemplary T cell expressed genes which can be cleaved by the methods described herein include the AAVS1 (i.e., PPP1R12C), TET2, FAS, BID, CTLA4, PDCD1, CBLB, PTPN6, CIITA, B2M, TRAC and TRBC genes, specifically TRAC.
  • the T cell expressed gene -targeting Cas9 ribonucleoprotein results in a reduction or elimination of expression of functional TRAC gene product (e.g., knockout of expression of functional TRAC gene product).
  • the T cell expressed gene is TRAC and wherein the guide RNA targets the 5’ end of the first exon of TRAC.
  • An exemplary guide RNA useful to target exon 1 of TRAC comprises SEQ ID NO: 9.
  • a non- viral double- stranded HDR template comprising the synthetic DNA sequence is introduced into the T cells.
  • viral vectors such as adeno-associated virus vectors have been used to provide the synthetic DNA template.
  • AAV vectors are expensive; (£>) could integrate viral genomes into the human genome; (c) trigger an immune response within the patient to viral components; (d) may result in highly variable transgene expression; and (d) take extended periods of time (e.g., months to years) to manufacture.
  • the non-viral double-stranded HDR template comprises the synthetic DNA sequence flanked by homology arms for insertion of the synthetic DNA sequence into the T cell expressed gene by the Cas9 RNP.
  • the homology arms have 50 to 3000 nucleotides in length and are complementary to sequences on either side of the cut site in the T cell expressed gene to facilitate incorporation of the synthetic DNA sequence into the genome of the T cell. Small sequence variations ( ⁇ 100 bases) from complementary sequences could be included to enable barcoding or tracking of various cell types.
  • the homology arms can comprise:
  • the non- viral double-stranded HDR template sequentially comprises a left homology arm- a splice acceptor site- a self-cleaving peptide sequence (e.g., a T2A coding sequence) - a CAR gene- a polyA terminator - a right homology arm.
  • a self-cleaving peptide sequence e.g., a T2A coding sequence
  • the splice acceptor site assists in the splicing of the synthetic DNA sequence into the transcript generated from the native T cell expressed gene.
  • the self-cleaving peptide sequence e.g., T2A
  • T2A assists in the separation or cleavage of the translated peptide of the protein product encoded by the synthetic DNA sequence from the protein product of the native T cell expressed gene.
  • exemplary selfcleaving peptides sequences include viral 2A peptides such as the a porcine teschovirus- 1 (P2A) peptide, a Thosea asigna virus (T2A) peptide, an equine rhinitis A virus (E2A) peptide, or a foot-and-mouth disease virus (F2A) peptide.
  • P2A porcine teschovirus- 1
  • T2A Thosea asigna virus
  • E2A equine rhinitis A virus
  • F2A foot-and-mouth disease virus
  • the polyA terminator e.g., a bovine growth hormone polyA.
  • the polyA terminator is a sequence-based element that defines the end of a transcriptional unit within the synthetic DNA sequence and initiate the process of releasing the newly synthesized RNA from the transcription machinery.
  • the non-viral double-stranded HDR template is produced by amplifying a sequence from a bacterial plasmid, e.g., SEQ ID NO: 1. Amplification can be done using a Q5® Hot Start Polymerase (NEB).
  • NEB Hot Start Polymerase
  • the double-stranded HDR template has an OD260 I OD280 of 1.8 to 2.1, and/or an OD2601 OD230 of 2.0 to 2.3.
  • the double-stranded HDR template has a concentration of 2000 to 10000 ng/pl.
  • the genome-edited T cells are deficient in expression of the T-cell expressed gene product, while expressing a gene product of the synthetic DNA sequence.
  • the endogenous promoter of the T-cell expressed gene can drive expression of a gene product within the synthetic DNA sequence.
  • the genome-edited T cells are then cultured in in xeno-free medium to provide a cultured population of T cells having the synthetic DNA sequence specifically integrated in the T-cell expressed gene locus.
  • xeno comes from the Greek “xenos” meaning strange.
  • Xeno-free or xenogeneic-free therefore means free from “strange” components, or components from a “strange” species (strange being relative to the native species you’re working with). In terms of cell culture, this would mean human cell lines can be cultured using human-derived components (like human serum), and it is considered xeno-free, since there is no difference between species.
  • culturing the genome-edited T cells in xeno-free medium can include recovery from integration of the synthetic DNA sequence and/or expansion of the edited T cell population.
  • the modified T cells can aggregate to form a cluster of cells.
  • Cells which exhibit a higher degree of aggregation typically recover at higher rates than cells that do not aggregate.
  • the aggregation could help cell-cell interaction through paracrine or juxtacrine signaling that assists in recovery.
  • the method further comprises imaging the population of CAR T cells and determining the degree of aggregation of the CAR T cells, and optionally selecting a population of aggregated CAR T cells.
  • culturing is done in round bottom culture wells at 20% of standard culture volume for the wells. It was unexpectedly found that by using round bottom culture wells rather than flat, for example, improved recovery was observed.
  • more than 4, 5, 6, 7, 8, 9 or 10 % of the population of unmodified T cells has the synthetic target gene inserted into their genomes.
  • an endogenous promoter of the T cell expressed gene drives expression of the synthetic DNA sequence
  • the synthetic DNA sequence can include a promoter that drives expression of the synthetic DNA sequence.
  • Exemplary promoters include CAGGS and EFl alpha.
  • the CAR T cells produced by the methods described herein have activity against an antigen on a solid tumor in vitro or in vivo.
  • a non- viral produced CAR T cell with a genome having a CAR sequence specifically integrated into a T cell expressed gene, wherein the T cell is enriched for the CD62L and/or CD45RA markers indicative of naive and stem cell memory phenotypes compared to viral-produced control CAR T cells. Also included is a non- viral produced CAR T cell with a genome having a CAR sequence specifically integrated into a T cell expressed gene, wherein the T cell has reduced expression of TIM3 and/or LAG3 markers of T cell exhaustion compared to viral-produced control CAR T cells.
  • the CD62L and/or CD45RA markers can be enriched more than 2-fold compared to the CD62L and/or CD45RA markers compared to viral-produced control CAR T cells.
  • the TIM3 and/or LAG3 markers are reduced more than 2-fold compared to the TIM3 and/or LAG3 markers compared to viral-produced control CAR T cells.
  • CAR T cell therapy for example, has been approved to treat hematologic malignancies like acute lymphoblastic leukemia, non-Hodgkin large B-cell lymphomas, and have been used to treat chronic lymphocytic leukemia and multiple myeloma.
  • CAR T cells are typically administered by intravenous infusion but could also be administered by subcutaneous, intratumoral, intraperitoneal or intracerebral injection.
  • Antibodies used in this study for flow cytometry and fluorescence activated cell sorting are listed in Table 1. Table 1: Antibodies used in flow cytometry and cell experiments
  • the tracr portion of the guide RNA is a proprietary 67mer tracr RNA available from IDT.
  • Dulbecco Modified Eagle Medium high glucose (Gibco) supplemented with 10% Fetal Bovine Serum (Gibco) and 1% Penicillin-Streptomycin.
  • AkaLuc-GFP CHLA-20 cells were a gift from the J. Thomson lab (UW-Madison).
  • PhoenixTM cells (ATCC) for viral preparation were maintained in DMEM (high glucose) supplemented with 10% Fetal Bovine Serum (Gibco), and selected using 1 pg/mL diphtheria toxin and 300
  • 3T3 cells were maintained in Dulbecco’s Modified Eagle Medium (Gibco) supplemented with 10% Fetal Bovine Serum (Gibco) and 1% Penicillin-Streptomycin (Gibco).
  • Cell authentication was performed using short tandem repeat analysis (Idexx BioAnalytics, Westbrook, ME) and per ATCC guidelines using morphology, growth curves, and Mycoplasma testing within 6 months of use using the e-Myco mycoplasma PCR detection kit (iNtRON Biotechnology Inc, Boca Raton, FL).
  • Cell lines were maintained in culture at 37°C in 5% CO2, and used after 3-5 passages in culture after thawing.
  • NV-AA V.S7-CAR An NV-AAVS7-CAR donor plasmid (SEQ ID NO: 1) was designed using a pAAV-CAGGS-GFP backbone (Addgene) and a 2kb CAR gBlock (IDT), which was inserted into the backbone using restriction cloning.
  • NV- 7 AC-CAR A 2kb region surrounding the TRAC locus was amplified by PCR from human genomic DNA and cloned into a pCR blunt II TOPOTM backbone (Thermo Fisher Scientific). The CAR transgene was then cloned into the TOPOTM TRAC vector using Gibson Assembly (NEB).
  • Double-stranded DNA HDRT production Plasmid constructs were used as PCR templates for NV (non viral) products.
  • NV-CAR and NV-mCh plasmids were MidiPrepped using the PureYield MidiPrep system (Promega).
  • PCR amplicons were generated from plasmid templates using Q5® Hot Start Polymerase (NEB), and pooled into 100 pl reactions for Solid Phase Reversible Immobilization (SPRI) cleanup (IX) using AMPure® XP beads according to the manufacturer’s instructions (Beckman Coulter). Each 100 pl starting product was eluted into 5 pl of water.
  • SPRI Solid Phase Reversible Immobilization
  • PCR products from round 1 cleanup were pooled and subjected to a second round of SPRI cleanup (IX) to increase total concentration; round 2 elution volume was 20% of round 1 input volume.
  • Template concentration and purity was quantified using NanoDropTM 2000 and QubitTM dsDNA BR Assays (Thermo Fisher Scientific), and templates were diluted in water to an exact concentration of 2 pg/pl.
  • SpyCas9 RNP preparation RNPs were produced by complexing a two- component gRNA to SpyCas9.
  • tracrRNA and crRNA were ordered from IDT, suspended in nuclease-free duplex buffer at 100 pM, and stored in single-use aliquots at - 80°C.
  • tracrRNA and crRNA were thawed, and 1 pl of each component was mixed 1: 1 by volume and annealed by incubation at 37°C for 30 minutes to form a 50 pM gRNA solution in individual aliquots for each electroporation replicate.
  • Recombinant sNLS-SpCas9-sNLS Cas9 (Aldevron, 10 mg/ml, total 0.8 pl) was added to the complexed gRNA at a 1:1 molar ratio and incubated for 15 minutes at 37 °C to form an RNP. Individual aliquots of RNPs were incubated for at least 30 seconds at room temperature with HDR templates for each sample prior to electroporation.
  • T cells were cultured at a density of 1 million cells/mL in ImmunoCultTM -XF T cell Expansion Medium (STEMCELL) supplemented with 200 U/mL IL-2 (Peprotech) and stimulated with ImmunoCultTM Human CD3/CD28/CD2 T cell Activator (STEMCELL) immediately after isolation, per the manufacturer’s instructions.
  • T cell culture Bulk T cells were cultured in ImmunoCultTM -XF T cell Expansion Medium at an approximate density of 1 million cells/mL. In brief, T cells were stimulated with ImmunoCultTM Human CD3/CD28/CD2 T cell Activator (STEMCELL) for 2 days prior to electroporation. On day 3, (24 hours post-electroporation), NV T and NV-mCh T cells were transferred to 1 mL of fresh culture medium (with 500 U/mL IL-2, without activator) and allowed to expand. T cells were passaged, counted, and adjusted to 1 million/mL in fresh medium + IL-2 on days 5 and 7 after isolation.
  • ImmunoCultTM Human CD3/CD28/CD2 T cell Activator STMCELL
  • NV T and NV-mCh T cells were transferred to 1 mL of fresh culture medium (with 500 U/mL IL-2, without activator) and allowed to expand. T cells were passaged, counted, and adjusted to 1 million
  • RV-CAR T cells were spinoculated with RV-CAR construct on day 3 and passaged on day 5 with the NV-CAR and NV-mCh T cells. Prior to electroporation or spinoculation, the medium was supplemented with 200 U/mL IL-2; post gene editing, medium was supplemented with 500 U/mL IL-2 (Peprotech).
  • T cell nucleofection RNPs and HDR templates were electroporated 2 days after T cell isolation and stimulation. During crRNA and tracrRNA incubation, T cells were centrifuged for 3 minutes at 200 g and counted using a CountessTM II FL Automated Cell Counter with 0.4% Trypan Blue viability stain (Thermo Fisher). 1 million cells per replicate were aliquoted into 1.5 mL tubes. During RNP complexation step (see RNP production), T cell aliquots were centrifuged for 10 min at 90g.
  • T cells were electroporated with a Lonza 4D NucleofectorTM with X Unit using pulse code EH115. Immediately after nucleofection, 80 pl of pre-warmed media with 500 U/mL IL-2 and 25 pl/mL ImmunoCultTM CD3/CD28/CD2 activator was added to each cuvette well. Cuvettes rested at 37°C in the cell culture incubator for 15 minutes. After 15 minutes, cells were moved to 200 pl total volume of media + IL-2 + activator (see Primary T cell culture above) in a round bottom 96 well plate.
  • Retrovirus production CAR retrovirus was manufactured using PhoenixTM(ATCC).
  • PhoenixTM ATCC
  • pSFG.iCasp9.2A.14G2A-CD28-OX40-CD3z plasmid was MidiPrepped using the PureYieldTM MidiPrep system (Promega).
  • One day prior to transfection selected PhoenixTM cells were plated on 0.01% Poly-L-Lysine coated 15 cm dishes at a density of 76,000 cells/cm 2 , or -65% confluency.
  • Retroviral transduction T cells for RV infection were cultured similarly to NV T and NV-mCh T cells, with two exceptions: 1) T cells were passaged and resuspended without ImmunocultTM CD2/CD28/CD3 activator on day 2 post-isolation, then spinoculated on Day 3. RV-CAR T cells were returned to the regular passaging schedule on day 5 postisolation. (See Fig. lb). Prior to spinoculation, non-treated cell culture 24 well plates were coated with Retronectin® according to the manufacturer’s instructions (Takara/Clontech).
  • T cells were centrifuged at 200 g for 3 minutes, counted, and resuspended to a concentration of 200,000 cells/mL, then stored in the incubator until plates were prepared.
  • Virus was added to Retronectin®-coated plates in a volume of 400 pl virus+ImmunoCultTM medium and centrifuged at 2000g for 2 hours at 32C.
  • 160,000 T cells in 800 pl were added to each well and spinoculated at 2000g for 60 minutes at 32°C, without brakes. T cells were then transferred to the incubator and left undisturbed for two days.
  • RV-CAR- TRAC-KO constructs cells were electroporated with RNPs on day 2 poststimulation and spinoculated on day 4 as described above, then allowed to rest until passage and transgene analysis at day 7.
  • CAR was detected using 1A7 anti-14G2a idiotype antibody (gift from Paul Sondel) conjugated to APC with the Lightning-Link® APC Antibody Labeling kit (Novus Biologicals). T cells were stained in BD BrilliantTM Stain Buffer (BD Biosciences). For panels including TRAC and CD3, cells were permeabilized and fixed using the BD Cytofix/CytopermTM Plus kit according to the manufacturer’s instructions.
  • Flow cytometry was performed on an AttuneTM NxT Flow cytometer, and fluorescence-activated cell sorting was performed on a BD FACS AriaTM. All antibodies used in this study are described in Table 1.
  • T cells from Donors 1 and 2 were stained and analyzed on day 9 of manufacture using fresh cells.
  • donors 3 and 4 only TCR, CAR, and CD62L were measured on day 9 of manufacture.
  • the change in protocol was made due to equipment restrictions related to institutional COVID-19 biosafety precautions, and CD62L was selected for analysis due to the known effects of cryopreservation on expression levels.
  • Genomic DNA was extracted from 100,000 cells per condition using DNA QuickExtractTM (Lucigen), and incubated at 65°C for 15 min, 68°C for 15 min, and 98°C for 10 min. Genomic integration of the CAR was confirmed by In-out PCR using a forward primer upstream of the TRAC left homology arm, and a reverse primer binding within the CAR sequence. Primer sequences are listed in Table 3. PCR was performed according to the manufacturer’s instructions using Q5® Hot Start Polymerase (NEB) using the following program: 98°C (30 s), 35 cycles of 98°C (10 s), 62°C (20 s), 72°C (2 min), and a final extension at 72 °C (2 min).
  • NEB Q5® Hot Start Polymerase
  • Next Generation Sequencing Indel formation at the TRAC locus was measured using Next Generation Sequencing (Illumina). Genomic PCR was performed according to the manufacturer’s instructions using Q5® Hot Start polymerase (NEB); primers are listed in Table 1. Products were purified using SPRI cleanup with AMPure® XP beads (Beckman Coulter), and sequencing indices were added with a second round of PCR using indexing primers (Illumina), followed by a second SPRI cleanup. Samples were pooled and sequenced on an Illumina® MiniSeq according to the manufacturer’s instructions. Analysis was performed using CRISPR RGEN.
  • Genome- wide, off-target analysis Genomic DNA from human primary CD4 + /CD8 + T cells was isolated using Gentra® Puregene® Kit (Qiagen) according to the manufacturer's instructions. CHANGE-seq was performed as described in the art. Briefly, purified genomic DNA was tagmented with a custom Tn5-transposome to an average length of 400 bp, followed by gap repair with Kapa HiFiTM HotStart Uracil-i- DNA Polymerase (KAPA Biosystems) and Taq DNA ligase (NEB). Gap-repaired tagmented DNA was treated with USER enzyme (NEB) and T4 polynucleotide kinase (NEB).
  • Intramolecular circularization of the DNA was performed with T4 DNA ligase (NEB) and residual linear DNA was degraded by a cocktail of exonucleases containing Plasmid-SafeTM ATP-dependent DNase (Lucigen), Lambda exonuclease (NEB) and Exonuclease I (NEB).
  • In vitro cleavage reactions were performed with 125 ng of exonuclease-treated circularized DNA, 90 nM of SpCas9 protein (NEB), NEB buffer 3.1 (NEB) and 270 nM of sgRNA, in a 50 pL volume.
  • Cleaved products were A-tailed, ligated with a hairpin adaptor (NEB), treated with USER enzyme (NEB) and amplified by PCR with barcoded universal primers NEBNext® Multiplex Oligos for Illumina® (NEB), using Kapa HiFiTM Polymerase (KAPA Biosystems). Libraries were quantified by qPCR (KAPA Biosystems) and sequenced with 151 bp paired-end reads on an Illumina® NextSeqTM instrument. CHANGE-seq data analyses were performed using open-source CHANGE-seq analysis software.
  • Cytokine Analysis Cytokine analysis is performed using a V-PLEX® Proinflammatory Panel 1 Human Kit (MSD, Catalog No K15049D-2) according to the manufacturer’s protocol. Measured cytokines include IFNy, IL- ip, IL-2, IL-4, IL-6, IL-8, IL- 10, IL-12p70, IL-13, and TNF-a. In brief, media was collected from the final day of cell culture before injection into mice and flash frozen and stored at -80°C. For co-culture samples, 250,000 T cells were co-cultured with 50,000 cancer cells in 250 pl ImmunoCultTM XF T cell expansion medium for 24 hours prior to media collection.
  • Fig. 2b 10,000 AkaLUC-GFP CHLA20 cells were seeded in triplicate per condition in a 96 well flat bottom plate. 48 hours later, 50,000 T cells were added to each well. 1 pl (0.05 pg) of CF® 594 Annexin V antibody (Biotium) was added to the wells. The plate was centrifuged at 100g for 1 minute and then placed in the IncuCyte® S3 Live-Cell Analysis System (Sartorius, Catalog No 4647), stored at 37°C, 5% CO2. Images were taken every 2 hours for 48 hours. Green object count was used to calculate the number of cancer cells in each well. Red object count was used to calculate the number of objects staining positive for Annexin V, an early apoptosis marker. Fluorescent images were analyzed with IncuCyte Base Analysis Software.
  • RNA sequencing 24 hours prior to assay, 200,000 AkaLUC- CHLA-20 cells were plated in 12 well plates and cultured overnight. One week after electroporation (day 9 post-isolation), T cells were counted and pooled into a single bank for all characterization studies (scRNA-seq, IncuCyte® cytotoxicity assay and in vivo experiments). Media was aspirated from cancer cells, and 1 million T cells in ImmunoCult T M-XF Medium + 500 U/mL IL-2 were seeded on the cancer cells, then cultured for 24 hours. A parallel culture of T cells without cancer cells was set up at the same T cell density in a separate 12 well plate.
  • co-culture cells were trypsinized for donor 1 and washed off the plate with media, and cells were singularized with a 35 pM cell strainer (Corning).
  • donor 2 co-culture cells were stained for CD45 and CAR, and FACS sorted into CD45 + CAR + and CD45 + CAR _ fractions prior to sample submission.
  • Cells were counted with a Countess II FL cell counter using trypan blue exclusion (Thermo Fisher Scientific), and samples were prepared for single cell RNA sequencing with the 10X Genomics 3’ kit (v3 chemistry) according to the manufacturer’s instructions. Libraries were sequenced using the Illumina® NovaSeqTM 6000 system.
  • FASTQ files were aligned with Cellranger v3.1.0 to custom reference genomes that included added sequences for the transgene(s) used in each culture condition (e.g. the NV TRAC_CAR HDRT sequence, AkaLuc-GFP, etc.). Downstream analyses were performed using Seurat 3. For each sample, cells either expressing the transgene of interest (CAR or mCherry) were identified, and transgenenegative cells were removed from the dataset. [0094] Gene set enrichment analysis (GSEA). GSEA was performed using the natural log-fold change values between sample pairs, using only the set of transgene-positive cells in each dataset. GSEA v.4.0.3 (Broad Institute) with the v7.1. Reactome signatures database from MSigDB was used with default parameters (1000 permutations). Data were exported and graphed in Microsoft Excel.
  • GSEA Gene set enrichment analysis
  • mice In vivo human neuroblastoma xenograft mouse model. All animal experiments were approved by the University of Wisconsin-Madison Animal Care and Use Committee (ACUC). Male and female NSG mice (9-25 weeks old) were subcutaneously injected with 10 million AkaLUC-GFP CHLA20 human neuroblastoma cells in the side flank to establish tumors. Six days later (Day 0), established tumors were verified by bioluminescence with the PerkinElmer In Vivo Imaging System (IVIS), and 10 million T cells were injected through the tail vein into each mouse. Mice were followed for weight loss and overall survival. On imaging days, mice were sedated using isoflurane and received intraperitoneal injections of -120 mg/kg D-luciferin (GoldBio).
  • IVIS PerkinElmer In Vivo Imaging System
  • mice were imaged via IVIS. Imaging was repeated every 3 to 4 days, starting 1 day before initial T cell injection (Day -1). Mice were injected with 100,000 IU of human IL-2 subcutaneously on day 0, day 4, and with each subsequent IVIS reading.
  • IxlO 6 cells were added to flow cytometry tubes in staining buffer (PBS with 2% FBS) and stained with antibodies for hCD45, mCD45, scFV 14G2a CAR, and PD-1 (see Table 1 for antibody information). The cells were then washed with PBS, centrifuged at 300g for 10 minutes, and 0.5ul of Ghost DyeTM Red 780 viability dye (Tonbo Biosciences) was added for 20 minutes at room temperature. Cells were then washed with staining buffer, spun down, and resuspended in 400 pl of staining buffer. Cells were then run on an AttuneTM NXT flow cytometer (Thermo Fisher Scientific). Subsequent analysis was performed using FlowjoTM software (BD). For donors 3 and 4, spleens and tumors were analyzed as mice reached euthanasia criteria and were stained with an extended antibody panel outlined in Table 1.
  • Described herein is a new method to insert CAR transgenes using Cas9 ribonucleoproteins (RNPs) targeted to a T-cell expressed gene locus such as the human TRAC locus in combination with a donor, specifically a PCR-amplified donor, encoding the CAR transgene (Fig. la).
  • the TRAC exon is SEQ ID Nos. 13 and 14.
  • HDRT HDR donor template
  • a splice acceptor followed by a self-cleaving peptide, 2A was cloned upstream of the GD2-CAR, and a transcriptional terminator followed by a poly A sequence was added downstream of the GD2-CAR.
  • a transcriptional terminator followed by a poly A sequence was added downstream of the GD2-CAR.
  • homology arms around the Cas9 cut site in targeted gene e.g., TRAC
  • the resulting novel donor construct within a plasmid is shown in FIG. 5.
  • the sequence of the TRAC-CAR is SEQ ID NO: 1.
  • dsDNA double-stranded DNA
  • dsDNA double-stranded DNA
  • dsDNA double-stranded DNA
  • Primary human T cells were electroporated with the HDR templates and Cas9 ribonucleoproteins (RNPs) targeting the human TRAC locus. Cells were subsequently expanded in xeno-free media and assayed on days 7 and 9 post-isolation (Fig. lb).
  • the viability of NV-CAR and RV-CAR T cells was comparably high (>80%) by the end of manufacturing (Fig. 3 a). Cell proliferation and growth over 9 days was robust for both groups (Fig. 3a).
  • MFI mean fluorescence intensity
  • next-generation sequencing of genomic DNA from the manufactured cell products confirmed high rates of indel formation at the TRAC locus, averaging 93.06% of reads for NV-CAR samples, and mirroring surface protein levels (Fig. 3c, d).
  • Proper genomic integration of the CAR was confirmed via “in-out” PCR amplification with primers specific to the TRAC locus and the transgene (Fig. 3e).
  • Highly sensitive genome-wide, off-target analysis for our editing strategy was assayed by CHANGE- seq.
  • the top identified modified locus was the intended on-target site (Fig. Ih, i) with a rapid drop-off for off-target modifications elsewhere in the genome (Data not shown).
  • the CHANGE-seq specificity ratio of our TRAC editing strategy is above average (0.056; 57th percentile) when compared to all editing strategies previously profiled by CHANGE-seq.
  • RNA-sequencing Single-cell RNA-sequencing (scRNA-seq) on 29,122 cells from two different donors at the end of the manufacturing process (data not shown).
  • scRNA-seq single-cell RNA-sequencing
  • Transgene -positive RV-CAR T cells exhibited elevated levels of transcripts associated with an exhausted T cell signature (high CTLA4, ENTPD1, LAG3, TIGIT, CD244-, Fig. 11) relative to transgene-positive NV-CAR T cells, but there were minimal significant differences in the exhaustion transcriptional profile between transgene-positive, donor- matched NV-CAR and NV-mCh T cells (Data not shown). Finally, we observed no significant changes in transcript levels for genes at or within 5 kb of off-target sites predicted by CHANGE-seq (Data not shown), indicating that any potential genomic disruptions at these sites did not lead to detectable changes in proximal transcripts.
  • Example 4 Cytokine production levels
  • RV-CAR T cells On day 9 of manufacturing, cytokine production levels were measured from the conditioned culture media. Prior to antigen exposure, RV-CAR T cells had higher levels of IFNy, TNFa, IE-2, IL-4, IL-10, and IL-13, in comparison to both the NV-CAR and NV- mCh T cells (Fig. 11). This result is consistent with the above transcriptional analysis showing hyperactive CAR signaling and recent observations that some RV-CAR T cells display elevated levels of tonic signaling prior to antigen exposure 15 .
  • NV-CAR T cells After a 24 h co-culture between the engineered T cells and GD2+ CHLA20 neuroblastoma, NV-CAR T cells either matched or surpassed the level of cytokine production of the RV-CAR T cells (Fig. 2a), indicating that NV-CAR T cells were capable of mounting a response to their target antigen, and suggesting that the RV-CAR T cells may be more exhausted prior to antigen exposure than the NV-CAR T cells.
  • IL-6 pre-antigen exposure and post-antigen exposure, were also observed for IL-6, IL-ip and IL-12p70, but not for IL-8 (Data not shown)
  • Example 5 In vitro potency of NV-CAR T cells
  • NV-CAR T cells demonstrate that NV-CAR T cells can properly achieve high levels of activation upon antigen exposure, while avoiding potentially detrimental high tonic-signaling prior to antigen exposure.
  • Tonic signaling is when intracellular signaling from both the TCR and CAR, in the absence of binding to the CAR target antigen, drives T cell phenotypes and differentiation toward effector or exhausted phenotypes given they both share common signaling pathways. Therefore, NV-CAR T cells that lack the TCR and have lower mean protein levels of the CAR could have lower intracellular tonic signaling, in the absence of binding to the CAR target antigen, relative to control viral CAR T cell products.
  • Example 6 In vivo potency of NV-CAR T cells
  • NV-CAR T cells persisted in both the spleens and tumors of the treated mice, but not for NV- mCh T cell treatments, indicating successful trafficking of NV-CAR T cells to the tumor microenvironment (Fig. 2h, Data not shown). Additionally, we observed that cells in the spleen had lower levels of PD-1 and TIM-3 exhaustion markers after NV-CAR treatment relative to the RV-CAR treatment (Fig. 2i), suggesting that the higher CAR MFI on RV- CARs (Fig. Id) and detrimental signaling after expansion (Fig.
  • a set of primers was used to amplify a longer double-stranded HDR template from the donor template plasmid of SEQ ID NO: 1.
  • This strategy generates a double-stranded HDR template length of 3.4 kb total, and the CAR knockin percentages have been consistently high as shown in Fig. 8.
  • the leftmost homology arm includes 588 bp of the TRAC locus directly upstream of the cutsite, and the rightmost homology arm includes 499 bases. These homology arms are longer than those from Example 2 which were 383 bp (left) and 391 bp (right). It was unexpected that increasing the length of the homology arms would increase the percentage of CAR knockin about 2-fold compared to the templates with shorter homology arms.
  • NV-CAR T cells exhibit proper TRAC -specific integration of the CAR transgene and an increased percentage and expression level of CD62L relative to conventional strategies.
  • Robust upregulation of gene transcripts prevalent in cytotoxic transcriptional programs and secretion of pro-inflammatory cytokines like IFNy and TNFa occur only after target antigen exposure, in contrast to conventional RV-CAR T cells that exhibit detrimental signaling during manufacturing.
  • NV-CAR T cells After injection into a GD2+ human neuroblastoma xenograft model, NV-CAR T cells induce strong regression of solid tumors compared to mock-edited T cells, and at levels comparable to RV-CAR T cells. NV-CAR T cells show reduced propensity to exhaustion at the gene expression and protein levels before antigen exposure, and at the protein level after antigen exposure.
  • FIG. 6 shows representative images of NV-CRISPR CAR T cells post-editing. Cells that demonstrate a high degree of aggregation are recovered at a higher rate. PCR donor refers to the HDRT. Aggregation can be indicative of successful genome editing and cell health, as non- aggregated cells are typically less viable with low to no levels of editing.

Abstract

Le titre est tel que fourni à la page 39 de la description.
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Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20170081650A1 (en) 2015-08-28 2017-03-23 The General Hospital Corporation Engineered CRISPR-Cas9 Nucleases
US20170152508A1 (en) 2013-03-15 2017-06-01 The General Hospital Corporation Using Truncated Guide RNAs (tru-gRNAs) to Increase Specificity for RNA-Guided Genome Editing
WO2021173925A1 (fr) * 2020-02-28 2021-09-02 Wisconsin Alumni Research Foundation Génération non virale de lymphocytes t récepteurs d'antigènes chimériques obtenus par édition génique

Patent Citations (3)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20170152508A1 (en) 2013-03-15 2017-06-01 The General Hospital Corporation Using Truncated Guide RNAs (tru-gRNAs) to Increase Specificity for RNA-Guided Genome Editing
US20170081650A1 (en) 2015-08-28 2017-03-23 The General Hospital Corporation Engineered CRISPR-Cas9 Nucleases
WO2021173925A1 (fr) * 2020-02-28 2021-09-02 Wisconsin Alumni Research Foundation Génération non virale de lymphocytes t récepteurs d'antigènes chimériques obtenus par édition génique

Non-Patent Citations (5)

* Cited by examiner, † Cited by third party
Title
"GenBank", Database accession no. YP_003082577
HU KE-JIA ET AL: "Combination of CRISPR/Cas9 System and CAR-T Cell Therapy: A New Era for Refractory and Relapsed Hematological Malignancies", CURRENT MEDICAL SCIENCE, HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY, WUHAN, vol. 41, no. 3, 1 June 2021 (2021-06-01), pages 420 - 430, XP037504426, ISSN: 2096-5230, [retrieved on 20210703], DOI: 10.1007/S11596-021-2391-5 *
ODÉ ZELDA ET AL: "CRISPR-Mediated Non-Viral Site-Specific Gene Integration and Expression in T Cells: Protocol and Application for T-Cell Therapy", CANCERS, vol. 12, no. 6, 26 June 2020 (2020-06-26), pages 1704, XP055804266, DOI: 10.3390/cancers12061704 *
PATRICK D. HSU ET AL: "Development and Applications of CRISPR-Cas9 for Genome Engineering", CELL, vol. 157, no. 6, 1 June 2014 (2014-06-01), Amsterdam NL, pages 1262 - 1278, XP055694974, ISSN: 0092-8674, DOI: 10.1016/j.cell.2014.05.010 *
ROTH THEODORE L ET AL: "Reprogramming human T cell function and specificity with non-viral genome targeting", NATURE, NATURE PUBLISHING GROUP UK, LONDON, vol. 559, no. 7714, 11 July 2018 (2018-07-11), pages 405 - 409, XP036544239, ISSN: 0028-0836, [retrieved on 20180711], DOI: 10.1038/S41586-018-0326-5 *

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